I don't have a solution, but I have more information for people who might have a solution.
Here are HMRCs notes for Reader 9: http://www.hmrc.gov.uk/ct/ct-online/file-return/online-change-settings.pdf
Michael, you may help by telling us what version of Reader you have.
The links you have posted are for the HMRC guidance I referred to in my original query. If you refer to step 12 in the guidance you have posted (for adobe reader version 10), it shows an image of the "trust" tab on "certifcate viewer" which has been accessed by going through "signature properties." In the image there are green ticks for "Execute high privelege Javacripts..." and "Perform priveleged system operations." On my version of the document there are red crosses for these two items, because I did not follow step 8 correctly (I did not check all of the appropriate boxes because I was using Adobe help on managing trusted identities rather than the HMRC guide). I have validated the signature but I am unable to go back and amend the privelege options because the option to "add to trusted identities" (see step 7) has been greyed out. Details on how to amend the information is not included in the HMRC guidance.
Can anyone help further?
On second thought don't worry! The V10 HMRC guidance does contain an explanation of how to amend the settings.